This guide results from the experience and lessons learned in co-designing thirteen technological services within the Cos4Cloud project. The technological services were created from a bottom-up approach, following a co-design process connected to an agile software development methodology. The co-design team implemented the co-design process as a service within the Cos4Cloud consortium, as stated in task 5.2. The result of implementing the co-design framework and methodologies and the corresponding monitoring during the co-design of the services, were evaluated and adapted to be shared with the citizen science community as a methodological guide. The present methodological guide includes an introduction to the world of co-design, where the main definitions and mindsets of co-design and design thinking are given, as well as some tools to start applying the creative methodologies within them. Secondly, it introduces the co-design methodology followed in Cos4Cloud, together with some important concepts, such as citizen science and citizen observatories. Then, a practical guide of implementation is given, including all the co-design methodologies used in Cos4Cloud. The most standard methods include a description and a work map template, while the customised ones incorporate a step-by-step guide to implement them. Finally, an explanation is given on how the co-design process was implemented in Cos4Cloud as a service for software developers, by using three interactive platforms that allowed us to perform all creative sessions. The document concludes with an invitation to implement co-design processes in other software development projects.